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- PDB-5gnx: The E171Q mutant structure of Bgl6 -

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Basic information

Entry
Database: PDB / ID: 5gnx
TitleThe E171Q mutant structure of Bgl6
ComponentsBeta-glucosidase
KeywordsHYDROLASE / glycosidase
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / beta-D-glucopyranose / PROPANOIC ACID
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXie, W. / Pang, P. / Cao, L.C. / Liu, Y.H. / Wang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
Guangdong Innovative Research Team ProgramNO. 2011Y038 China
Fundamental Research Funds for the Central Universities16lgjc76 China
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structures of a glucose-tolerant beta-glucosidase provide insights into its mechanism.
Authors: Pang, P. / Cao, L.C. / Liu, Y.H. / Xie, W. / Wang, Z.
History
DepositionJul 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-glucosidase
B: Beta-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3737
Polymers105,7722
Non-polymers6015
Water16,268903
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.247, 95.697, 94.976
Angle α, β, γ (deg.)90.00, 125.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-glucosidase /


Mass: 52886.172 Da / Num. of mol.: 2 / Mutation: E171Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: beta-glucosidase
#2: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 903 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 8K, 600 mM NaCl, 100 mM Tris-HCl pH 8.0, 1M glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 84462 / % possible obs: 98.5 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.042 / Net I/σ(I): 48.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 25.8 / CC1/2: 0.993 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PHENIXdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OIN

1oin


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.676 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.089
RfactorNum. reflection% reflectionSelection details
Rfree0.15117 4151 5 %RANDOM
Rwork0.12275 ---
obs0.12419 79066 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.629 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å21.07 Å2
2---2.15 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7184 0 40 903 8127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197466
X-RAY DIFFRACTIONr_bond_other_d0.0010.026789
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.93310174
X-RAY DIFFRACTIONr_angle_other_deg2.356315564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17922.976373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.822151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.241563
X-RAY DIFFRACTIONr_chiral_restr0.2240.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218579
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021860
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8531.7163613
X-RAY DIFFRACTIONr_mcbond_other1.8471.7153612
X-RAY DIFFRACTIONr_mcangle_it2.3432.5564518
X-RAY DIFFRACTIONr_mcangle_other2.3442.5574519
X-RAY DIFFRACTIONr_scbond_it3.3022.0013853
X-RAY DIFFRACTIONr_scbond_other3.30323830
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7732.875623
X-RAY DIFFRACTIONr_long_range_B_refined5.84215.779688
X-RAY DIFFRACTIONr_long_range_B_other5.84315.7619675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 288 -
Rwork0.128 5633 -
obs--95.04 %

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